Retrieving gene ontology information from Ensembl
In this recipe, you will learn how to use gene ontology information again by querying the Ensembl REST API. Gene ontologies are controlled vocabularies for annotating genes and gene products. These are made available as trees of concepts (with more general concepts near the top of the hierarchy). There are three domains for gene ontologies: the cellular component, the molecular function, and the biological process.
Getting ready
As with the previous recipe, we do not require any pre-downloaded data, but since we are using web APIs, internet access will be needed. The amount of data that will be transferred will be limited.
As usual, you can find this content in the Chapter05/Gene_Ontology.py notebook file. We will make use of the do_request function, which was defined in Step 1 of the previous recipe (Finding orthologues with the Ensembl REST API). To draw GO trees, we will use pygraphviz, a graph-drawing library:
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